Re: [Freesurfer] building a pipeline using mri_robust_register and other FS functions
Thanks Bruce and Martin. Martin, I have a followup question: Let's say I run mri_robust_register with --iscale flag and also use --halfmov and --halfdst flags to create two outputs hm.mgz and hd.mgz 1) You mentioned that --iscale "adjusts the intensities of both input images to better match". Are the image intensities of the outputs hm.mgz and hd.mgz also adjusted to match each other ? Also here is brief description (in case someone else is looking for something similar) Basically, I have 2 scans of the same subject and I need three steps: (1) skull-stripping, (2) intensity normalization between time-points and (3) registration of time-points; (following your recommendation, I put skull removal before registration) For the intensity normalization, ideally, a good option would be to do a "histogram matching" between the two time-points. However, I am guessing that the mri_normalize would be a good first approximation/substitute to the histogram matching step. (I did see mri_histo_eq function but I am not sure if I should use that instead of mri_normalize.) Alternatively, Bruce suggested I could use the FS longitudinal pipeline and compare the norm.mgz images for each time-point from the longitudinal data. I like this approach better since the longitudinal stream maps all the timepoints to the template space and I can look for changes in the template space. Thanks Mehul On Wed, Jan 25, 2012 at 1:45 PM, Martin Reuter wrote: > Hi Mehul, > > - if lesions show large changes, normalization might be dangerous > - mri_robust_register has a flag --iscale for global intensity > adjustment (a global scaling parameter that adjusts the intensity images > of both inputs to better match) > - mri_normalize, normalized the white matter to be around 110 is that > what you want? > - usually registration will be more accurate if images are skull > stripped. > > Best, Martin > > On Tue, 2012-01-24 at 09:39 -0800, Mehul Sampat wrote: > > Hi Folks, > > We have subjects with high lesion load which changes significantly > > over time. > > I want to use FS functions to build a pipeline for comparing lesion > > changes in two time-points of the same-subject. > > I am thinking of using the following steps; > > > > > > 1) Use mri_normalize to normalize the two time-points. > > 2) Use mri_robust_register to register two time-points of the same > > subject to half-way space. > > 3) Use mri_skull_strip > > 4) Use subtraction imaging or some other techniques to look for lesion > > changes. > > > > > > > > > > My questions are: > > 1) I think I need mri_normalize since the output from > > mri_robust_register is not intensity normalized ? > > 2) Instead of the first three steps, I could also do the following: > > Run autorecon1 for both timepoints and then run mri_robust_register > > on the skull stripped images > > Does it matter if we run mri_robust_register before or after skull > > stripping ? > > > > > > Thanks > > Mehul > > > > > > > > > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] building a pipeline using mri_robust_register and other FS functions
Hi Mehul, - if lesions show large changes, normalization might be dangerous - mri_robust_register has a flag --iscale for global intensity adjustment (a global scaling parameter that adjusts the intensity images of both inputs to better match) - mri_normalize, normalized the white matter to be around 110 is that what you want? - usually registration will be more accurate if images are skull stripped. Best, Martin On Tue, 2012-01-24 at 09:39 -0800, Mehul Sampat wrote: > Hi Folks, > We have subjects with high lesion load which changes significantly > over time. > I want to use FS functions to build a pipeline for comparing lesion > changes in two time-points of the same-subject. > I am thinking of using the following steps; > > > 1) Use mri_normalize to normalize the two time-points. > 2) Use mri_robust_register to register two time-points of the same > subject to half-way space. > 3) Use mri_skull_strip > 4) Use subtraction imaging or some other techniques to look for lesion > changes. > > > > > My questions are: > 1) I think I need mri_normalize since the output from > mri_robust_register is not intensity normalized ? > 2) Instead of the first three steps, I could also do the following: > Run autorecon1 for both timepoints and then run mri_robust_register > on the skull stripped images > Does it matter if we run mri_robust_register before or after skull > stripping ? > > > Thanks > Mehul > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] building a pipeline using mri_robust_register and other FS functions
Hi Mehul why not just run the longitudinal stream, then subtract the longitudinal results? I would probably look at the subtraction of the norm.mgz. cheers Bruce On Tue, 24 Jan 2012, Mehul Sampat wrote: Hi Folks,We have subjects with high lesion load which changes significantly over time. I want to use FS functions to build a pipeline for comparing lesion changes in two time-points of the same-subject. I am thinking of using the following steps; 1) Use mri_normalize to normalize the two time-points. 2) Use mri_robust_register to register two time-points of the same subject to half-way space. 3) Use mri_skull_strip 4) Use subtraction imaging or some other techniques to look for lesion changes. My questions are: 1) I think I need mri_normalize since the output from mri_robust_register is not intensity normalized ? 2) Instead of the first three steps, I could also do the following: Run autorecon1 for both timepoints and then run mri_robust_register on the skull stripped images Does it matter if we run mri_robust_register before or after skull stripping ? Thanks Mehul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] building a pipeline using mri_robust_register and other FS functions
Hi Folks, We have subjects with high lesion load which changes significantly over time. I want to use FS functions to build a pipeline for comparing lesion changes in two time-points of the same-subject. I am thinking of using the following steps; 1) Use mri_normalize to normalize the two time-points. 2) Use mri_robust_register to register two time-points of the same subject to half-way space. 3) Use mri_skull_strip 4) Use subtraction imaging or some other techniques to look for lesion changes. My questions are: 1) I think I need mri_normalize since the output from mri_robust_register is not intensity normalized ? 2) Instead of the first three steps, I could also do the following: Run autorecon1 for both timepoints and then run mri_robust_register on the skull stripped images Does it matter if we run mri_robust_register before or after skull stripping ? Thanks Mehul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
